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Sample GSM913975 Query DataSets for GSM913975
Status Public on Aug 18, 2012
Title NFATc1-deficient osteoclasts rep2
Sample type RNA
 
Source name mouse osteoclast culture, day 3 MCSF/RANKL
Organism Mus musculus
Characteristics cell type: bone marrow macrophage derived osteoclasts
strain: C57BL/6
genotype: NFATc1 fl/fl MxCre+
Treatment protocol Osteoclat precursor cultures were cultured in the presence of MCSF and RANKL for 3 days to generate early osteoclasts.
Growth protocol Osteoclast precursors were purified from whole bone marrow of n=3 mice (replicate 1) or n=4 mice (replicate 2) by flow cytometric sorting for CD11b- CD3e- B220- ckit+cfms+ cell s and plated at 20,000/24well plate in alpha-meM with mCSF and RANKL.
Extracted molecule total RNA
Extraction protocol RNAeasy extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Description gene expression data in osteoclast cultures
Data processing The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
 
Submission date Apr 12, 2012
Last update date Aug 19, 2012
Contact name Julia F. Charles
E-mail(s) jfcharles@partners.org
Organization name Brigham and Women's Hospital
Department Division of Rheumatology, Immunology and Allergy
Lab Antonios O. Aliprantis Lab
Street address 75 Francis Street, Smith Building 6th floor
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL8321
Series (1)
GSE37219 Comparison expression data from wild-type and NFATc1-deficient osteoclasts

Data table header descriptions
ID_REF
VALUE MAS5.0 signal intensity
ABS_CALL

Data table
ID_REF VALUE ABS_CALL
AFFX-BioB-5_at 152.4 P
AFFX-BioB-M_at 195.8 P
AFFX-BioB-3_at 128.6 P
AFFX-BioC-5_at 358 P
AFFX-BioC-3_at 485.2 P
AFFX-BioDn-5_at 1046.4 P
AFFX-BioDn-3_at 2175.4 P
AFFX-CreX-5_at 5925.2 P
AFFX-CreX-3_at 7291.1 P
AFFX-DapX-5_at 23.4 P
AFFX-DapX-M_at 17.6 A
AFFX-DapX-3_at 3.3 A
AFFX-LysX-5_at 0.6 A
AFFX-LysX-M_at 3 A
AFFX-LysX-3_at 11.4 A
AFFX-PheX-5_at 5.4 A
AFFX-PheX-M_at 2.2 A
AFFX-PheX-3_at 18.4 A
AFFX-ThrX-5_at 6.5 A
AFFX-ThrX-M_at 4.6 A

Total number of rows: 22690

Table truncated, full table size 421 Kbytes.




Supplementary file Size Download File type/resource
GSM913975_NFATc1_KO2.CEL.gz 2.3 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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